PIGR-1, a member of immunoglobulin gene superfamily

ABSTRACT

PIGR-1 polypeptides and polynucleotides and methods for producing such polypeptides by recombinant techniques are disclosed. Also disclosed are methods for utilizing PIGR-1 polypeptides and polynucleotides in the design of protocols for the treatment of rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), among others and diagnostic assays for such conditions.

This application is a division of U.S. application Ser. No. 08/955,937, filed Oct. 22, 1997, now U.S. Pat. No. 6,020,161. which claims the benefit of U.S. Provisional Application No. 60/056,152, filed Aug. 19, 1997 the entire contents of which are incorporated herein by reference.

FIELD OF INVENTION

This invention relates to newly identified polynucleotides, polypeptides encoded by them and to the use of such polynucleotides and polypeptides, and to their production. More particularly, the polynucleotides and polypeptides of the present invention relate to Immunoglobulin superfamily, hereinafter referred to as PIGR-1. The invention also relates to inhibiting or activating the action of such polynucleotides and polypeptides.

BACKGROUND OF THE INVENTION

The immunoglobulin (Ig) gene superfamily comprises a large number of cell surface glycoproteins that share sequence homology with the V and C domians of antibody heavy and light chains. These molecules function as receptors for antigen, immunoglobulin and cytokines as well as adhesion molecules (A. F. Williams et al., Annu. Rev. Immunol. 6:381-405, 1988).

Most Ig superfamily members are relatively complex polydomain molecules cotaining multiple Ig V- and C-like domains (T. Hunkapiller et al., Adv. Immunol. 44:1-63, 1989). However, a subset of them have relatively simple structures containing only a single Ig domain in the extracellular region. Examples of this type of receptors are CD28 and CD8 (A. Aruffo et al., Proc. Natl. Acad. Sci. USA 84:8573-8577, 1987) Recently, CMRF-35, an novel membrane glycoprotein of the Ig gene superfamily containing a single extracellular Ig V domain, was identified by D. G. Jackson et al., Eur. J. Immunol. 22:1157-1163, 1992. CMRF-35 is exclusively detected on cells from both the myeloid and lymphoid differentiation pathways. However, expression of this gene is markedly influenced by stimulation of leucocytes with mitogens and cytokines (A. Daish et al., Immunology 79:55-63, 1993). This suggests that CMRF-35 may be strongly associated with differentiation and proliferation of diverse leucocytes types. This indicates that these receptors have an established, proven history as therapeutic targets. Clearly there is a need for identification and characterization of further receptors which can play a role in preventing, ameliorating or correcting dysfunctions or diseases, including, but not limited to, rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and Inflammatory Bowel Disease (IBD).

SUMMARY OF THE INVENTION

In one aspect, the invention relates to PIGR-1 polypeptides and recombinant materials and methods for their production. Another aspect of the invention relates to methods for using such PIGR-1 polypeptides and polynucleotides. Such uses include the treatment of rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), among others. In still another aspect, the invention relates to methods to identify agonists and antagonists using the materials provided by the invention, and treating conditions associated with PIGR-1 imbalance with the identified compounds. Yet another aspect of the invention relates to diagnostic assays or detecting diseases associated with inappropriate PIGR-1 activity or levels.

DESCRIPTION OF THE INVENTION

Definitions

The following definitions are provided to facilitate understanding of certain terms used frequently herein.

“PIGR-1” refers, among others, to a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2, or an allelic variant thereof.

“Receptor Activity” or “Biological Activity of the Receptor” refers to the metabolic or physiologic function of said PIGR-1 including similar activities or improved activities or these activities with decreased undesirable side-effects. Also included are antigenic and immunogenic activities of said PIGR-1.

“PIGR-1 gene” refers to a polynucleotide comprising the nucleotide sequence set forth in SEQ ID NO:1 or allelic variants thereof and/or their complements.

“Antibodies” as used herein includes polyclonal and monoclonal antibodies, chimeric, single chain, and humanized antibodies, as well as Fab fragments, including the products of an Fab or other immunoglobulin expression library.

“Isolated” means altered “by the hand of man” from the natural state. If an “isolated” composition or substance occurs in nature, it has been changed or removed from its original environment, or both. For example, a polynucleotide or a polypeptide naturally present in a living animal is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is “isolated”, as the term is employed herein.

“Polynucleotide” generally refers to any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. “Polynucleotides” include, without limitation single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. In addition, “polynucleotide” refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The term polynucleotide also includes DNAs or RNAs containing one or more modified bases and DNAs or RNAs with backbones modified for stability or for other reasons. “Modified” bases include, for example, tritylated bases and unusual bases such as inosine. A variety of modifications has been made to DNA and RNA; thus, “polynucleotide” embraces chemically, enzymatically or metabolically modified forms of polynucleotides as typically found in nature, as well as the chemical forms of DNA and RNA characteristic of viruses and cells. “Polynucleotide” also embraces relatively short polynucleotides, often referred to as oligonucleotides.

“Polypeptide” refers to any peptide or protein comprising two or more amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres. “Polypeptide” refers to both short chains, commonly referred to as peptides, oligopeptides or oligomers, and to longer chains, generally referred to as proteins. Polypeptides may contain amino acids other than the 20 gene-encoded amino acids. “Polypeptides” include amino acid sequences modified either by natural processes, such as posttranslational processing, or by chemical modification techniques which are well known in the art. Such modifications are well described in basic texts and in more detailed monographs, as well as in a voluminous research literature. Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. It will be appreciated that the same type of modification may be present in the same or varying degrees at several sites in a given polypeptide. Also, a given polypeptide may contain many types of modifications. Polypeptides may be branched as a result of ubiquitination, and they may be cyclic, with or without branching. Cyclic, branched and branched cyclic polypeptides may result from posttranslation natural processes or may be made by synthetic methods. Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cystine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proeolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. See, for instance, PROTEINS—STRUCTURE AND MOLECULAR PROPERTIES, 2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York, 1993 and Wold, F., Posttranslational Protein Modifications: Perspectives and Prospects, pgs. 1-12 in POSTTRANSLATION COVALENT MODIFICATION OF PROTEINS, B. C. Johnson, Ed., Academic Press, Now York, 1983; Seifter et al., “Analysis for protein modifications and nonprotein cofactors”, Meth Enzymol (1990) 182:626-646 and Rattan et al., “Protein Synthesis: Posttranslational Modifications and Aging”, Ann NY Acad Sci (1992) 663:48-62.

“Variant” as the term is used herein, is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, but retains essential properties. A typical variant of a polynucleotide differs in nucleotide sequence from another, referenced polynucleotide. Changes in the nucleotide sequence of the variant may or may not alter the amino acid sequence of a polypeptide encoded by the reference polynucleotide. Nucleotide changes may result in amino acids substitutions, additions, deflections, fusions and truncations in the polypeptide encoded by the reference sequence, as discussed below. A typical variant of a polypeptide differs in amino acid sequence from another, reference polypeptide. Generally, differences are limited so that the sequences of the reference polypeptide and the variant are closely overall and, in many regions, identical. A variant and reference polypeptide may differ in amino acid sequence by one or more substitutions, additions, deletions in any combination. A substituted or inserted amino acid residue may or may not be one encoded by the genetic code. A variant of a polynucleotide or polypeptide may be a naturally occurring such as an allelic variant, or it may be a variant that is not known to occur naturally. Non-naturally occurring variants of polynucleotides and polypeptides may be made by mutagenesis techniques or by direct synthesis.

“Identity” is a measure of the identity of nucleotide sequences or amino acid sequences. In general, the sequences are aligned so that the highest order match is obtained. “Identity” per se has an art-recognized meaning and can be calculated using published techniques. See, e.g.: (COMPUTATIONAL MOLECULAR BIOLOGY, Lesk, A. M., ed., Oxford University Press, New York, 1988; BIOCOMPUTING: INFORMATICS AND GENOME PROJECTS, Smith, D. W., ed., Academic Press, New York, 1993; COMPUTER ANALYSIS OF SEQUENCE DATA, PART I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; SEQUENCE ANALYSIS IN MOLECULAR BIOLOGY, von Heinje, G., Academic Press, 1987; and SEQUENCE ANALYSIS PRIMER, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991). While there exist a number of methods to measure identity between two polynucleotide or polypeptide sequences, the term “identity” is well known to skilled artisans (Carillo, H., and Lipton, D., SIAM J Applied Math (1988) 48:1073). Methods commonly employed to determine identity or similarity between two sequences include, but are not limited to, those disclosed in Guide to Huge Computers, Martin J. Bishop, ed., Academic Press, San Diego, 1994, and Carillo, H., and Lipton, D., SIAM J Applied Math (1988) 48:1073. Methods to determine identity and similarity are codified in computer programs. Preferred computer program methods to determine identity and similarity between two sequences include, but are not limited to, GCS program package (Devereux, J., et al., Nucleic Acids Research (1984) 12(1):387), BLASTP, BLASTN, FASTA (Atschul, S. F. et al., J Molec Biol (1990) 215:403).

As an illustration, by a polynucleotide having a nucleotide sequence having at least, for example, 95% “identity” to a reference nucleotide sequence of SEQ ID NO: 1 is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence of SEQ ID NO: 1. In other words, to obtain a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. These mutations of the reference sequence may occur at the 5 or 3 terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence.

Similarly, by a polypeptide having an amino acid sequence having at least, for example, 95% “identity” to a reference amino acid sequence of SEQ ID NO:2 is intended that the amino acid sequence of the polypeptide is identical to the reference sequence except that the polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the reference amino acid of SEQ ID NO: 2. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a reference amino acid sequence, up to 5% of the amino acid residues in the reference sequence may be deleted or substituted with another amino acid, or a number of amino acids up to 5% of the total amino acid residues in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.

Polypeptides of the Invention

In one aspect, the present invention relates to PIGR-1 polypeptides (or PIGR-1 proteins). The PIGR-1 polypeptides include the polypeptides of SEQ ID NOS:2 and 4; as well as polypeptides comprising the amino acid sequence of SEQ ID NO:2; and polypeptides comprising the amino acid sequence which have at least 80% identity to that of SEQ ID NO:2 over its entire length, and still more preferably at least 90% identity, and even still more preferably at least 95% identity to SEQ ID NO: 2. Furthermore, those with at least 97-99% are highly preferred. Also included within PIGR-1 polypeptides are polypeptides having the amino acid sequence which have at least 80% identity to the polypeptide having the amino acid sequence of SEQ ID NO: 2 over its entire length, and still more preferably at least 90% identity, and even still more preferably at least 95% identity to SEQ ID NO: 2. Furthermore, those with at least 97-99% are highly preferred. Preferably PIGR-1 polypeptides exhibit at least one biological activity of the receptor.

The PIGR-1 polypeptides may be in the form of the “mature” protein or may be a part of a larger protein such as a fusion protein. It is often advantageous to include an additional amino acid sequence which contains secretory or leader sequences, pro-sequences, sequences which aid in purification such as multiple histidine residues, or an additional sequence for stability during recombinant production.

Fragments of the PIGR-1 polypeptides are also included in the invention. A fragment is a polypeptide having an amino acid sequence that entirely is the same as part, but not all, of the amino acid sequence of the aforementioned PIGR-1 polypeptides. As with PIGR-1 polypeptides, fragments may be “free standing,” or comprised within a larger polypeptide of which they form a part or region, most preferably as a single continuous region. Representative examples of polypeptide fragments of the invention, include, for example, fragments from about amino acid number 1-20, 21-40, 41-60, 61-80, 81-100, and 101 to the end of PIGR-1 polypeptide. In this context “about” includes the particularly recited ranges larger or smaller by several, 5, 4, 3, 2 or 1 amino acid at either extreme or at both extremes.

Preferred fragments include, for example, truncation polypeptides having the amino acid sequence of PIGR-1 polypeptides, except for deletion of a continuous series of residues that includes the amino terminus, or a continuous series of residues that includes the carboxyl terminus or deletion of two continuous series of residues, one including the amino terminus and one including the carboxyl terminus. Also preferred are fragments characterized by structural or functional attributes such as fragments that comprise alpha-helix and alpha-helix forming regions, beta-sheet and beta-sheet-forming regions, turn and turn-forming regions, coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic index regions. Other preferred fragments are biologically active fragments. Biologically active fragments are those that mediate receptor activity, including those with a similar activity or an improved activity, or with a decreased undesirable activity. Also included are those that are antigenic or immunogenic in an animal, especially in a human.

Preferably, all of these polypeptide fragments retain the biological activity of the receptor, including antigenic activity. Among the most preferred fragment is that having the amino acid sequence of SEQ ID NO: 4. Variants of the defined sequence and fragments also form part of the present invention. Preferred variants are those that vary from the referents by conservative amino acid substitutions—i.e., those that substitute a residue with another of like characteristics. Typical such substitutions are among Ala, Val, Leu and Ile; among Ser and Thr, among the acidic residues Asp and Glu; among Asn and Gln; and among the basic residues Lys and Arg; or aromatic residues Phe and Tyr. Particularly preferred are variants in which several, 5-10, 1-5, or 1-2 amino acids are substituted, deleted, or added in any combination.

The PIGR-1 polypeptides of the invention can be prepared in any suitable manner. Such polypeptides include isolated naturally occurring polypeptides, recombinantly produced polypeptides, synthetically produced polypeptides, or polypeptides produced by a combination of these methods. Means for preparing such polypeptides are well understood in the art.

Polynucleotides of the Invention

Another aspect of the invention relates to PIGR-1 polynucleotides. PIGR-1 polynucleotides include isolated polynucleotides which encode the PIGR-1 polypeptides and fragments, and polynucleotides closely related thereto. More specifically, PIGR-1 polynucleotide of the invention include a polynucleotide comprising the nucleotide sequence contained in SEQ ID NO:1 encoding a PIGR-1 polypeptide of SEQ ID NO: 2, and polynucleotides having the particular sequences of SEQ ID NOS:1 and 3. PIGR-1 polynucleotides further include a polynucleotide comprising a nucleotide sequence that has at least 80% identity over its entire length to a nucleotide sequence encoding the PIGR-1 polypeptide of SEQ ID NO: 2, and a polynucleotide comprising a nucleotide sequence that is at least 80% identical to that of SEQ ID NO:1 over its entire length. In this regard, polynucleotides at least 90% identical are particularly preferred, and those with at least 95% are especially preferred Furthermore, those with at least 97% are highly preferred and those with at least 98-99% are most highly preferred, with at least 99% being the most preferred. Also included under PIGR-1 polynucleotides are a nucleotide sequence which has sufficient identity to a nucleotide sequence contained in SEQ ID NO:1 to hybridize under conditions useable for amplification or for use as a probe or marker. The invention also provides polynucleotides which are complementary to such PIGR-1 polynucleotides.

PIGR-1 of the invention is structurally related to other proteins of the Immunoglobulin superfamily, as shown by the results of sequencing the cDNA encoding human PIGR-1. The cDNA sequence of SEQ ID NO:1 contains an open reading frame (nucleotide number 132 to 734) encoding a polypeptide of 201 amino acids of SEQ ID NO:2. The amino acid sequence of Table 2 (SEQ ID NO:2) has about 42.65% identity (using BLASTX) in 67 amino acid residues with CMRF35 (D. G. Jackson et al., Eur. J. Immunol. 22:1157-1163, 1992). Furthermore, PIGR-1 (SEQ ID NO:2) is 30% identical to the poly-Ig receptor over 90 amino acid residues (P. Krajci et al., Biochem. Biophys. Res. Commun. 158:783-789, 1989). The nucleotide sequence of Table 1 (SEQ ID NO:1) has about 68.64% identity (using BLASTN) in 118 nucleotide residues with Human CMRF35 mRNA (D. G. Jackson et al., Eur. J. Immunol. 22:1157-1163, 1992). Thus, PIGR-1 polypeptides and polynucleotides of the present invention are expected to have, inter alia, similar biological functions/properties to their homologous polypeptides and polynucleotides, and their utility is obvious to anyone skilled in the art.

TABLE 1^(a) 1 CCGGGTCGAC CCACGCGTCC GTGTGCAGAA GGTGCAAGCC AGAGCTCAGG 51 CAGAACTTCC AGAGTGCATC TGGGATCTGC ATTTGCCACT GGTTGCAGAT 101 CAGGCGGACG AGGAGCCGGG AAGGCAGAGC CATGTGGCTG CCCCCTGCTC 151 TGCTCCTTCT CAGCCTCTCA GGCTGTTTCT CCATCCAAGG CCCAGAGTCT 201 GTGAGAGCCC CAGAGCAGGG GTCCCTGACG GTTCAATGCC ACTATAAGCA 251 AGGATGGGAG ACCTACATTA AGTGGTGGTG CCGAGGGGTG CGCTGGGATA 301 CATGCAAGAT CCTCATTGAA ACCAGAGGGT CGGAGCAAGG AGAGAAGAGT 351 GACCGTGTGT CCATCAAGGA CAATCAGAAA GACCGCACGT TCACTGTGAC 401 CATGGAGGGG CTCAGGCGAG ATGACGCAGA TGTTTACTGG TGTGGGATTG 451 AAAGAAGAGG ACCTGACCTT GGGACTCAAG TGAAAGTGAT TGTTGACCCA 501 GAGGGAGCGG CTTCCACAAC AGCAAGCTCA CCTACCAACA GCAATATGGC 551 AGTGTTCATC GGCTCCCACA AGAGGAACCA CTACATGCTC CTGGTATTTG 601 TGAAGGTGCC CATCTTGCTC ATCTTGGTCA CTGCCATCCT CTGGTTGAAG 651 GGGTCTCAGA GGGTCCCTGA GGAGCCAGGG GAACAGCCTA TCTACATGAA 701 CTTCTCCGAA CCTCTGACTA AAGACATGGC CACTTAGAGA GATGGATCTG 751 CAGAGCCTTC CTGCCCTGGC CACGTTTCCA GAAGAGACTC GGGCTGTGGA 801 AGGAACATCT ACGAGTCCTC GGGATGCAGT GACTGAGATA GGGGCCCTGG 851 GCCTCCGCCC TGGCCTTGGA GCTGGTGGGC ACCTCCCTGT TCTGCACAGC 901 TCAGGGACTT AGCCAGGTCC TCTCCTGAGC CACCATCACC TCCTGGGGTG 951 CCAGCACCTG TTCTCTTGGT CAGGAGCTGT AGAGATGGAG CTCAAGCACT 1001 GGACGACTCT GTCCCCACTG CTGGAATAAC TCGGGCACAG AGCATGGGAC 1051 CAAAGTACAG AAAGAGGTTG GGGGAGACCC CCCCAGCCCT AGACTTCCAT 1101 CATTCCGGAG ACCAACTCAA CACCGTCTTT GCCTGAGAAC CTGATATATC 1151 CGTGTTTTTA AATTTTTTTT TTTCTAGCAA AGTTGGGTTT TAATGACTTA 1201 TGTTCATAGG AAACCTCTCT GATCCCACAC ACAAGGAGGG TGATTCTGGG 1251 ATGAGTTCCT GGTTCTAGGG CATGAGGGGC TGGATGGACC CTGTCCCCAG 1301 GGAGGACATG GCTCTGAGTC CACAGGGCTG AGGAGGCAAT GGGAACCTCC 1351 CTGGCCCGGC CCGGTGGTTG GCCTCCCCCT CCCACCTCTT CCTCCTCCTA 1401 GCTCCCCAAG CTCCCTGCCT ATTCCCCCAC CTCCGAGGGG CTGCAGCTTG 1451 GGAGCCTCCT CAGCATGACA GCTTGGGTCT CCTCCCCAAA AGAGCCTGTC 1501 AGGCCTCAAG AACCACCTCC AGGTGGGGAG GGCAGTAACG AAAACCATCG 1551 CAGGAAATGG CACCCTCCCT TTTCGGTGAT GTTGAAATCA TGTTACTAAT 1601 GAAAACTGTC CTAGGGAAGT GGTTCTGTCT CCTCACAGGC TTCACCCACG 1651 GCGATGAGGC CCTTGAATGT GGTCACTTTG TGCTGTATGG TTGAGGGACC 1701 CTCACACCAA AGGGACCTTC CCATGTGAGA TGTGCTCCCG CCCCCACCTG 1751 CCCACAAGCA AACACACCAC ACATGTTCGG CATGTTGCCG TTTGAACACC 1801 CATGAGGACG CCTCCAACCT GCTCTTGGTT CTAATAGGGA GTACTGACTG 1851 TCAGCAGTGG ATAAAGGAGA GGGGACCCTC TGGTCCCTAG CATGGCACCC 1901 AGAGCCTCCC CTCTTCTTGT CCTTCAGCCA AAGAGAAACT TTCTCTGACT 1951 TTGAACTGAA TTTAGGTCTC TGGCCAATGA TGGGCCTGAA AATTCCATAA 2001 TGGCCAGAGA GGAGAGTTCG AGCCCGGCTA AGATCCCCTG AGTCATTCTG 2051 TGAGGGACCA AGACCCACAG TCCACCAGCC CCAGGGCCCT ACCTCCTGGA 2101 ATGCTTTCCT GGATCCAGCT TCCCGAAGAT CCGACCAGAC CCAGGGAGGA 2151 CGGCACCGCT CCGCGGGAGG GAAAGCCAAA GCATGGTGCT TCACCAGCTG 2201 GACTCAGGGG CGAGGGGACA TGGGCGCTTG TCAACGTGAT GTCATTCTTT 2251 TCCCACCGTT TCTTCCTGTT GATATTCAAT GAATCCGTCA ATCTCTCTGG 2301 AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAA ^(a)nucleotide sequence of a human PIGR-1 (SEQ ID NO:1).

TABLE 2^(b) 1 MWLPPALLLL SLSGCFSIQG PESVRAPEQG SLTVQCHYKQ GWETYIKWWC 51 RGVRWDTCKI LIETRGSEQG EKSDRVSIKD NQKDRTFTVT MEGLRRDDAD 101 VYWCGIERRG PDLGTQVKVI VDPEGAASTT ASSPTNSNMA VFIGSHKRNH 151 YMLLVFVKVP ILLILVTAIL WLKGSQRVPE EPGEQPIYMN FSEPLTKDMA 201 T ^(b)amino acid sequence of a human PIGR-1 (SEQ ID NO:2).

One polynucleotide of the present invention encoding PIGR-1 may be obtained using standard cloning and screening, from a cDNA library derived from mRNA in cells of human bone marrow, macrophage, eosinophil, activated neutrophils and T cells using the expressed sequence tag (EST) analysis (Adams, M. D. et al., Science (1991) 252:1651-1656; Adams, M. D. et al., Nature, (1992) 355:632-634; Adams M. D., et al., Nature (1995) 377 Supp:3-174). Polynucleotides of the invention can also be obtained from natural sources such as genomic DNA libraries or can be synthesized using well commercially available techniques.

The nucleotide sequence encoding PIGR-1 polypeptide of SEQ ID NO:2 may be identical to the polypeptide encoding sequence contained in Table 1 (nucleotide number 132 to 734 of SEQ ID NO:1), or it may be a sequence, which as a result of the redundancy (degeneracy) of the genetic code, also encodes the polypeptide of SEQ ID NO:2.

When the polynucleotides of the invention are used for the recombinant production of PIGR-1 polypeptide, the polynucleotide may include the coding sequence for the mature polypeptide or a fragment thereof, by itself; the coding sequence for the mature polypeptide or fragment in reading frame with other coding, sequences, such as those encoding a leader or secretory sequence, a pre-, or pro- or prepro-protein sequence, or other fusion peptide portions. For example, a marker sequence which facilitates purification of the fused polypeptide can be encoded. In certain preferred embodiments of this aspect of the invention, the marker sequence is a hexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.) and described in Gentz et al., Proc Natl Acad Sci USA (1989) 86:821-824, or is an HA tag. The polynucleotide may also contain non-coding 5′ and 3′ sequences, such as transcribed, non-translated sequences, splicing and polyadenylation signals, ribosome binding sites and sequences that stabilize mRNA.

Further preferred embodiments are polynucleotides encoding PIGR-1 variants comprising the amino acid sequence of PIGR-1 polypeptide of Table 2 (SEQ ID NO:2) in which several, 5-10, 1-5, 1-3, 1-2 or 1 amino acid residues are substituted, deleted or added, in any combination. Among the preferred polynucleotides of the present invention is contained in Table 3 (SEQ ID NO: 3) encoding the amino acid sequence of Table 4 (SEQ ID NO: 4).

TABLE 3^(c) 1 TGTGCAGAAG GTGCAAGCCA GAGCTCAGGC AGAACTTCCA GAGTGCATCT 51 GGGATCTGCA TTTGCCACTG GTTGCAGATC AGGCGGACGA GGAGCCGGGA 101 AGGCAGAGCC ATGTGGCTGC CCCCTGCTCT GCTCCTTCTC AGCCTCTCAG 151 GCTGTTTCTC CATCCAAGGC CCAGAGTCTG TGAGAGCCCC AGAGCAGGGG 201 TCCCTGACGG TTCAATGCCA CTATAAGCAA GGATGGGAGA CCTACATTAA 251 GTGGTGGTGC CGAGGGGTGC GCTGGGATAC ATGCAAGATC CTCATTGAAA 301 CCAGAGGGTC GGAGCAAGGA GAGAAGAGTG ACCGTGTGTC CATCAAGGAC 351 AATCAGAAAG ACCGCACGTT CACTGTGACC ATGGAGGGGC TCAGGCGAGA 401 TGACGCAGAT GTTTACTGGT GTGGGATTGA AAGAAGAGGA CCTGACCTTG 451 GGACTCAAGT GAAAATTGAT TGTTNACCCA GAGGGAGCGG CTTTCCACAA 501 CAGCAAAGCT CACCTACCAA CAGCAATATG GCAGTGTTCA TCGGCTCCCA 551 CAAGAGGAAC CACTACATGC TCCTGGTATT TGTGAAGGTG CCCATCTTGC 601 TCATCTTGGT CAATGCCATN CTCTGGTTGA AAGGGTCTCA GAGGGTCCCT 651 GAGGAGCCAN GGGAACAGCC TATCTACATG GACTTCTCCG GACTCTGACT 701 AAAGACAT ^(c)A partial nucleotide sequence of a human PIGR-1 (SEQ ID NO:3).

TABLE 4^(d) 1 MWLPPALLLL SLSGCFSIQG PESVRAPEQG SLTVQCHYKQ GWETYIKWWC 51 RGVRWDTCKI LIETRGSEQG EKSDRVSIKD NQKDRTFTVT MEGLRRDDAD 101 VYWCGIERRG PDLGTQVKID CXPRGSGFPQ QQSSPTNSNM AVFIGSHKRN 151 HYMLLVFVKV PILLILVNAX LWLKGSQRVP EEPXEQPIYM DFSGL ^(d)A partial amino acid sequence of a human PIGR-1 (SEQ ID NO:4).

The present invention further relates to polynucleotides that hybridize to the herein above-described sequences. In this regard, the present invention especially relates to polynucleotides which hybridize under stringent conditions to the herein above-described polynucleotides. As herein used, the term “stringent conditions” means hybridization will occur only if there is at least 80%, and preferably at least 900%, and more preferably at least 95%, yet even more preferably 97-99% identity between the sequences.

Polynucleotides of the invention, which are identical or sufficiently identical to a nucleotide sequence contained in SEQ ID NO:1 or a fragment thereof, may be used as hybridization probes for cDNA and genomic DNA, to isolate full-length cDNAs and genomic clones encoding PIGR-1 and to isolate cDNA and genomic clones of other genes (including genes encoding homologs and orthologs from species other than human) that have a high sequence similarity to the PIGR-1 gene. Such hybridization techniques are known to those of skill in the art. Typically these nucleotide sequences are 80% identical, preferably 90% identical, more preferably 95% identical to that of the referent. The probes generally will comprise at least 15 nucleotides. Preferably, such probes will have at least 30 nucleotides and may have at least 50 nucleotides. Particularly preferred probes will range between 30 and 50 nucleotides.

In one embodiment, to obtain a polynucleotide encoding PIGR-1 polypeptide, including homologs and orthologs from species other than human, comprises the steps of screening an appropriate library under stingent hybridization conditions with a labeled probe having the SEQ ID NO: 1 or a fragment thereof (including that of SEQ ID NO: 3), and isolating full-length cDNA and genomic clones containing said polynucleotide sequence. Such hybridization techniques are well known to those of skill in the art. Stringent hybridization conditions are as defined above or alternatively conditions under overnight incubation at 42° C. in a solution comprising: 50% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 microgram/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1×SSC at about 65° C.

The polynucleotides and polypeptides of the present invention may be employed as research reagents and materials for discovery of treatments and diagnostics to animal and human disease.

Vectors, Host Cells, Expression

The present invention also relates to vectors which comprise a polynucleotide or polynucleotides of the present invention, and host cells which are genetically engineered with vectors of the invention and to the production of polypeptides of the invention by recombinant techniques. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention.

For recombinant production, host cells can be genetically engineered to incorporate expression systems or portions thereof for polynucleotides of the present invention. Introduction of polynucleotides into host cells can be effected by methods described in many standard laboratory manuals, such as Davis et al., BASIC METHODS IN MOLECULAR BIOLOGY (1986) and Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989) such as calcium phosphate transfection, DEAE-dextran mediated transfection, transvection, microinjection, cationic lipid-mediated transfection, electroporation, transduction, scrape loading, ballistic introduction or infection.

Representative examples of appropriate hosts include bacterial cells, such as streptococci, staphylococci, E. coli, Streptomyces and Bacillus subtilis cells; fungal cells, such as yeast cells and Aspergillus cells; insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, HEK 293 and Bowes melanoma cells; and plant cells.

A great variety of expression systems can be used. Such systems include, among others, chromosomal, episomal and virus-derived systems, e.g., vectors derived from bacterial plasmids, from bacteriophage, from transposons, from yeast episomes, from insertion elements, from yeast chromosomal elements, from viruses such as baculoviruses, papova viruses, such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids. The expression systems may contain control regions that regulate as well as engender expression. Generally, any system or vector suitable to maintain, propagate or express polynucleotides to produce a polypeptide in a host may be used. The appropriate nucleotide sequence may be inserted into an expression system by any of a variety of well-known and routine techniques, such as, for example, those set forth in Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL (supra).

For secretion of the translated protein into the lumen of the endoplasmic reticulum, into the periplasmic space or into the extracellular environment, appropriate secretion signals may be incorporated into the desired polypeptide. These signals may be endogenous to the polypeptide or they may be heterologous signals.

If the PIGR-1 polypeptide is to be expressed for use in screening assays, generally, it is preferred that the polypeptide be produced at the surface of the cell. In this event, the cells may be harvested prior to use in the screening assay. If PIGR-1 polypeptide is secreted into the medium, the medium can be recovered in order to recover and purify the polypeptide; if produced intracellularly, the cells must first be lysed before the polypeptide is recovered.

PIGR-1 polypeptides can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Most preferably, high performance liquid chromatography is employed for purification. Well known techniques for refolding proteins may be employed to regenerate active conformation when the polypeptide is denatured during isolation and or purification.

Diagnostic Assays

This invention also relates to the use of PIGR-1 polynucleotides for use as diagnostic reagents. Detection of a mutated form of PIGR-1 gene associated with a dysfunction will provide a diagnostic tool that can add to or define a diagnosis of a disease or susceptibility to a disease which results from under-expression, over-expression or altered expression of PIGR-1. Individuals carrying mutations m the PIGR-1 gene may be detected at the DNA level by a variety of techniques.

Nucleic acids for diagnosis may be obtained from a subject's cells, such as from blood, urine, saliva, tissue biopsy or autopsy material. The genomic DNA may be used directly for detection or may be amplified enzymatically by using PCR or other amplification techniques prior to analysis. RNA or cDNA may also be used in similar fashion. Deletions and insertions can be detected by a change in size of the amplified product in comparison to the normal genotype. Point mutations can be identified by hybridizing amplified DNA to labeled PIGR-1 nucleotide sequences. Perfectly matched sequences can be distinguished from mismatched duplexes by RNase digestion or by differences in melting temperatures. DNA sequence differences may also be detected by alterations in electrophoretic mobility of DNA fragments in gels, with or without denaturing agents, or by direct DNA sequencing. See, e.g., Myers et al., Science (1985) 230:1242. Sequence changes at specific locations may also be revealed by nuclease protection assays, such as RNase and S1 protection or the chemical cleavage method. See Cotton et al., Proc Natl Acad Sci USA (1985) 85: 4397-4401. In another embodiment, an array of oligonucleotides probes comprising PIGR-1 nucleotide sequence or fragments thereof can be constructed to conduct efficient screening of e.g., genetic mutations. Array technology methods are well known and have general applicability and can be used to address a variety of questions in molecular genetics including gene expression, genetic linkage, and genetic variability. (See for example: M. Chee et al., Science, Vol 274, pp 610-613 (1996)).

The diagnostic assays offer a process for diagnosing or determining a susceptibility to rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and imflammatory bowel disease (IBD) through detection of mutation in the PIGR-1 gene by the methods described

In addition, rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), can be diagnosed by methods comprising determining from a sample derived from a subject an abnormally decreased or increased level of PIGR-1 polypeptide or PIGR-1 mRNA. Decreased or increased expression can be measured at the RNA level using any of the methods well known in the art for the quantitation of polynucleotides, such as, for example, PCR, RT-PCR, RNase protection, Northern blotting and other hybridization methods. Assay techniques that can be used to determine levels of a protein, such as an PIGR-1, in a sample derived from a host are well-known to those of skill in the art. Such assay methods include radioimmunoassays, competitive-binding assays, Western Blot analysis and ELISA assays.

Thus in another aspect, the present invention relates to a diagonostic kit for a disease or suspectability to a disease, particularly rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), which comprises:

(a) a PIGR-1 polynucleotide, preferably the nucleotide sequence of SEQ ID NO: 1, or a fragment thereof;

(b) a nucleotide sequence complementary to that of (a);

(c) a PIGR-1 polypeptide, preferably the polypeptide of SEQ ID NO: 2, or a fragment thereof; or

(d) an antibody to a PIGR-1 polypeptide, preferably to the polypeptide of SEQ ID NO: 2.

It will be appreciated that in any such kit, (a), (b), (c) or (d) may comprise a substantial component.

Chromosome Assays

The nucleotide sequences of the present invention are also valuable for chromosome identification. The sequence is specifically targeted to and can hybridize with a particular location on an individual human chromosome. The mapping of relevant sequences to chromosomes according to the present invention is an important first step in correlating those sequences with gene associated disease. Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. Such data are found, for example, in V. McKusick, Mendelian Inheritance in Man (available on line through Johns Hopkins University Welch Medical Library). The relationship between genes and diseases that have been mapped to the same chromosomal region are then identified through linkage analysis (coinheritance of physically adjacent genes). The differences in the cDNA or genomic sequence between affected and unaffected individuals can also be determined. If a mutation is observed in some or all of the affected individuals but not in any normal individuals, then the mutation is likely to be the causative agent of the disease.

Antibodies

The polypeptides of the invention or their fragments or analogs thereof, or cells expressing them can also be used as immunogens to produce antibodies immunospecific for the PIGR-1 polypeptides. The term “immunospecific” means that the antibodies have substantiall greater affinity for the polypeptides of the invention than their affinity for other related polypeptides in the prior art.

Antibodies generated against the PIGR-1 polypeptides can be obtained by administering the polypeptides or epitope-bearing fragments, analogs or cells to an animal, preferably a nonhuman, using routine protocols. For preparation of monoclonal antibodies, any technique which provides antibodies produced by continuous cell line cultures can be used. Examples include the hybridoma technique (Kohler, G. and Milstein, C., Nature (1975) 256:495-497), the trioma technique, the human B-cell hybridoma technique (Kozbor et al., Immunology Today (1983) 4:72) and the EBV-hybridoma technique (Cole et al., MONOCLONAL ANTIBODIES AND CANCER THERAPY, pp. 77-96, Alan R. Liss, Inc., 1985).

Techniques for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can also be adapted to produce single chain antibodies to polypeptides of this invention. Also, transgenic mice, or other organisms including other mammals, may be used to express humanized antibodies.

The above-described antibodies may be employed to isolate or to identify clones expressing the polypeptide or to purify the polypeptides by affinity chromatography.

Antibodies against PIGR-1 polypeptides may also be employed to treat rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), among others.

Vaccines

Another aspect of the invention relates to a method for inducing an immunological response in a mammal which comprises inoculating the mammal with PIGR-1 polypeptide, or a fragment thereof, adequate to produce antibody and/or T cell immune response to protect said animal from rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), among others. Yet another aspect of the invention relates to a method of inducing immunological response in a mammal which comprises, delivering PIGR-1 polypeptide via a vector directing expression of PIGR-1 polynucleotide in vivo in order to induce such an immunological response to produce antibody to protect said animal from diseases.

Further aspect of the invention relates to an immunological/vaccine formulation (composition) which, when introduced into a mammalian host, induces an immunological response in that mammal to a PIGR-1 polypeptide wherein the composition comprises a PIGR-1 polypeptide or PIGR-1 gene. The vaccine formulation may further comprise a suitable carrier. Since PIGR-1 polypeptide may be broken down in the stomach, it is preferably administered parenterally (including subcutaneous, intramuscular, intravenous, intradermal etc. injection). Formulations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the recipient; and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents. The formulations may be presented in unit-dose or multi-dose containers, for example, sealed ampoules and vials and may be stored in a freeze-dried condition requiring only the addition of the sterile liquid carrier immediately prior to use. The vaccine formulation may also include adjuvant systems for enhancing the immunogenicity of the formulation, such as oil-in water systems and other systems known in the art. The dosage will depend on the specific activity of the vaccine and can be readily determined by routine experimentation.

Screening Assays

The PIGR-1 polypeptide of the present invention may be employed in a screening process for compounds which bind the receptor and which activate (agonists) or inhibit activation of (antagonists) the receptor polypeptide of the present invention. Thus, polypeptides of the invention may also be used to assess the binding of small molecule substrates and ligands in, for example, cells, cell-free preparations, chemical libraries, and natural product mixtures. These substrates and ligands may be natural substrates and ligands or may be structural or functional mimetics. See Coligan et al., Current Protocols in Immunology 1(2):Chapter 5 (1991).

PIGR-1 polypeptides are responsible for many biological functions, including many pathologies. Accordingly, it is desirous to find compounds and drugs which stimulate PIGR-1 on the one hand and which can inhibit the function of PIGR-1 on the other hand. In general, agonists are employed for therapeutic and prophylactic purposes for such conditions as rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD) Antagonists may be employed for a variety of therapeutic and prophylactic purposes for such conditions as rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD).

In general, such screening procedures involve producing appropriate cells which express the receptor polypeptide of the present invention on the surface thereof. Such cells include cells from mammals, yeast, Drosophila or E. coli. Cells expressing the receptor (or cell membrane containing the expressed receptor) are then contacted with a test compound to observe binding, or stimulation or inhibition of a functional response.

The assays may simply test binding of a candidate compound wherein adherence to the cells bearing the receptor is detected by means of a label directly or indirectly associated with the candidate compound or in an assay involving competition with a labeled competitor. Further, these assays may test whether the candidate compound results in a signal generated by activation of the receptor, using detection systems appropriate to the cells bearing the receptor at their surfaces. Inhibitors of activation are generally assayed in the presence of a known agonist and the effect on activation by the agonist by the presence of the candidate compound is observed.

Further, the assays may simply comprise the steps of mixing a candidate compound with a solution containing a PIGR-1 polypeptide to form a mixture, measuring PIGR-1 activity in the mixture, and comparing the PIGR-1 activity of the mixture to a standard.

The PIGR-1 cDNA, protein and antibodies to the protein may also be used to configure assays for detecting the effect of added compounds on the production of PIGR-1 mRNA and protein in cells. For example, an ELISA may be constructed for measuring secreted or cell associated levels of PIGR-1 protein using monoclonal and polyclonal antibodies by standard methods known in the art, and this can be used to discover agents which may inhibit or enhance the production of PIGR-1 (also called antagonist or agonist, respectively) from suitably manipulated cells or tissues. Standard methods for conducting screening assays are well understood in the art.

Examples of potential PIGR-1 antagonists include antibodies or, in some cases, oligonucleotides or proteins which are closely related to the ligand of the PIGR-1, e.g., a fragment of the ligand, or small molecules which bind to the receptor but do not elicit a response, so that the activity of the receptor is prevented.

Thus in another aspect, the present invention relates to a screening kit for identifying agonists, antagonists, ligands, receptors, substrates, enzymes, etc. for PIGR-1 polypeptides; or compounds which decrease or enhance the production of PIGR-1 polypeptides, which comprises:

(a) a PIGR-1 polypeptide, preferably that of SEQ ID NO:2;

(b) a recombinant cell expressing a PIGR-1 polypeptide, preferably that of SEQ ID NO:2;

(c) a cell membrane expressing a PIGR-1 polypeptide; preferably that of SEQ ID NO: 2; or

(d) antibody to a PIGR-1 polypeptide, preferably that of SEQ ID NO: 2.

It will be appreciated that in any such kit, (a), (b), (c) or (d) may comprise a substantial component.

Prophylactic and Therapeutic Methods

This invention provides methods of treating an abnormal conditions related to both an excess of and insufficient amounts of PIGR-1 activity.

If the activity of PIGR-1 is in excess, several approaches are available. One approach comprises administering to a subject an inhibitor compound (antagonist) as hereinabove described along with a pharmaceutically acceptable carrier in an amount effective to inhibit activation by blocking binding of ligands to the PIGR-1, or by inhibiting a second signal, and thereby alleviating the abnormal condition.

In another approach, soluble forms of PIGR-1 polypeptides still capable of binding the ligand in competition with endogenous PIGR-1 may be administered. Typical embodiments of such competitors comprise fragments of the PIGR-1 polypeptide.

In still another approach, expression of the gene encoding endogenous PIGR-1 can be inhibited using expression blocking techniques. Known such techniques involve the use of antisense sequences, either internally generated or separately administered. See, for example, O'Connor, J Neurochem (1991) 56:560 in Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988). Alternatively, oligonucleotides which form triple helices with the gene can be supplied. See, for example, Lee et al., Nucleic Acids Res (1979) 6:3073; Cooney et al., Science (1988) 241:456; Dervan et al., Science (1991) 251:1360. These oligomers can be administered per se or the relevant oligomers can be expressed in vivo.

For treating abnormal conditions related to an under-expression of PIGR-1 and its activity, several approaches are also available. One approach comprises administering to a subject a therapeutically effective amount of a compound which activates PIGR-1, i.e., an agonist as described above, in combination with a pharmaceutically acceptable carrier, to thereby alleviate the abnormal condition. Alternatively, gene therapy may be employed to effect the endogenous production of PIGR-1 by the relevant cells in the subject. For example, a polynucleotide of the invention may be engineered for expression in a replication defective retroviral vector, as discussed above. The retroviral expression construct may then be isolated and introduced into a packaging cell transduced with a retroviral plasmid vector containing RNA encoding a polypeptide of the present invention such that the packaging cell now produces infectious viral particles containing the gene of interest. These producer cells may be administered to a subject for engineering cells in vivo and expression of the polypeptide in vivo. For overview of gene therapy, see Chapter 20, Gene Therapy and other Molecular Genetic-based Therapeutic Approaches, (and references cited therein) in Human Molecular Genetics, T Strachan and A P Read, BIOS Scientific Publishers Ltd (1996).

Formulation and Administration

Peptides, such as the soluble form of PIGR-1 polypeptides, and agonists and antagonist peptides or small molecules, may be formulated in combination with a suitable pharmaceutical carrier. Such formulations comprise a therapeutically effective amount of the polypeptide or compound, and a pharmaceutically acceptable carrier or excipient. Such carriers include but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof. Formulation should suit the mode of administration, and is well within the skill of the art. The invention further relates to pharmaceutical packs and kits comprising one or more containers filled with one or more of the ingredients of the aforementioned compositions of the invention.

Polypeptides and other compounds of the present invention may be employed alone or in conjunction with other compounds, such as therapeutic compounds.

Preferred forms of systemic administration of the pharmaceutical compositions include injection, typically by intravenous injection. Other injection routes, such as subcutaneous, intramuscular, or intraperitoneal, can be used. Alternative means for systemic administration include transmucosal and transdermal administration using penetrants such as bile salts or fusidic acids or other detergents. In addition, if properly formulated in enteric or encapsulated formulations, oral administration may also be possible. Administration of these compounds may also be topical and/or localized, in the form of salves, pastes, gels and the like.

The dosage range required depends on the choice of peptide, the route of administration, the nature of the formulation, the nature of the subject's condition, and the judgment of the attending practitioner. Suitable dosages, however, are in the range of 0.1-100 μg/kg of subject. Wide variations in the needed dosage, however, are to be expected in view of the variety of compounds available and the differing efficiencies of various routes of administration. For example, oral administration would be expected to require higher dosages than administration on by intravenous injection. Variations in these dosage levels can be adjusted using standard empirical routines for optimization, as is well understood in the art.

Polypeptides used in treatment can also be generated endogenously in the subject, in treatment modalities often referred to as “gene therapy” as described above. Thus, for example, cells from a subject may be engineered with a polynucleotide, such as a DNA or RNA, to encode a polypeptide ex vivo, and for example, by the use of a retroviral plasmid vector. The cells are then introduced into the subject.

EXAMPLES

The examples below are carried out using standard techniques, which are well known and routine to those of sill in the art, except where otherwise described in detail. The examples illustrate, but do not limit the invention.

Example 1

While there are several methods to obtain the full length cDNA, two are outlined below.

1) The method of Rapid Amplification of cDNA Ends (RACE) can be utilized to obtain the 5′ end. See Frohman et al., Proc. Nat. Acad. Sci USA 85, 8998-9002. (1988). Briefly, specific oliognucleotides are annealed to mRNA and used to prime the synthesis of the cDNA strand. Following destruction of the mRNA with RNaseH, a poly C anchor sequence is added to the 3′ end of the cDNA and the resulting fragment is amplified using a nested set of antisense primers and an anchor sequence primer. The amplified fragment is cloned into an appropriate vector and subjected to restriction and sequence analysis.

2) The polymerase chain reaction can be used to amplify the 5′ end of the cDNA from human cDNA libraries using sequential rounds of nested PCR with two sets of primers. One set of antisense primers is specific to the 5′ end of the partial cDNA and the other set of primers anneals to a vector specific sequence. The amplified products are cloned into an appropriate vector and subjected to restriction and sequence analysis.

Example 2

PIGR-1 Belongs to Immunoglobulin (Ig) Superfamily

The extracellular region of PIGR-1 contains a single Ig domain with a V-like fold as shown by (1) the presence of Ig V fold conserved residues and (2) homology to several other Ig like proteins (poly Ig V1 and V4, CMRF35, TCR Vβ and Ig κ V_(L)).

In the following alignment, conserved Ig V residues are shown in bold and residues in PIGR-1 shared with at least 3 of the other members are noted with a *.

                B             C          C′      C″ PIGR-1 IQGPESVAAPEQGS{overscore (LTVQCHYK+L )} QGWETY GV{overscore (RWDTCKILI+L )} ET{overscore (RGSEQ+L )} GEKS{overscore (DR+L )} 75 (AA 18-75 of SEQ ID NO:2) PolyIgRV1 IFGPEEVNSVEGNSVSITCYYPPTSVNTRKYWC.RQGARG..CITLISSEGYVSSKYAGR 57 (SEQ ID NO:5) PolyIgRV4 PRSPTVVKGVAGSSVAVLCPYNRKESKSIKYWCLWEGAQNGRCPLLVDSEGWVKAQYEGR 60 (SEQ ID NO:6) CMRF35 LSHPMTVAGPVGGSLSVQCRYEKEHRTLNKFWC..RPPQILRCDKIVETKGS.AGKRNGR 56 (SEQ ID NO:7) TCR vβ SQKPSRDICQRGTSLTIQCQV.DSQVTMMFWYRQQPGQSLTLIATANQGSEATYESGFVI 60 (SEQ ID NO:8) Ig k V_(L) TQTPASVEVAVGGTVTIKCQASQSISTYLSWYQQKPGQRPKLLIY....RASTLASG.VS 56 (SEQ ID NO:9)   *  *      *    * *     *  * **   *     *       *        *    D        E               F PIGR-1 {overscore (VSIKDN)}QK{overscore (DRTF.TVTME)}GLRRDDA{overscore (DVYWCGIER)}RGPDLGTQVKVIV (AA 76-121 of SEQ ID NO:2) PolyIgRV1 ANLTNFPENGTF.TVILNQLSQDDSGRYKCGLGINSRGLSFDVSLEV (SEQ ID NO:10) PolyIgV4 LSLLEEPGNGTF.TVILNQLTSRDAGFYWC...LTNGDTLWRTTVEI (SEQ ID NO:11) CMRF35 VSIRDSPANLSF.TVTLENLTEEDAGTYWCGVDTPWLRDFHDPIVEV (SEQ ID NO:12) TCR vβ DKFPISRPNLTFSTLTVSNMSPEDSSIYLCSVE..GEAGDTQY.FGP (SEQ ID NO:13) Ig k V_(L) SRFKGSGSGTEF.TLTISGVECADAATYYCQQGWSSSNVEN...VFG (SEQ ID NO:14)           ** ***   *   **  * *              *

Example 3

PIGR-1 Gene Expression Pattern

PIGR-1, a new member of the Ig superfamily, has been identified. The predicted protein sequence of this new gene shows modest, but extended, homology to CMRF-35, particularly in the extracellular domain. Based on the library source of the EST sequences comprising PIGR-1 which were isolated from leucocytes such as macrophage, neutrophil, eosinophil and T cells, its expression is restricted to leucocytes, suggesting a role in immune function. Thus, this protein is a candidate target for diseases of the immune system such as rheumatoid arthritis (RA), multiple sclerosis (MS), psoriasis, systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD).

Example 4

Recombinant Soluble PIGR-1 Proteins

The extracellular domain of PIGR-1 is expressed as a secreted soluble protein by truncation at the start of the transmembrane domain (asparagine 149 or histidine 150 in Table 2) as has been described for other immunoglobulin domain proteins, e.g. for CD4 (K. C. Deen et al., Nature 331: 82-84 (1988)). PIGR-1 is also expressed as a secreted, soluble Ig fusion protein by linking the same extracellular region of PIGR-1 to the hinge and constant domains of heavy chain IgG such as has been described for CD4 (D. J. Capon et al., Nature 317: 525-531 (1989)). In addition, preparation of oligomeric Ig fusion proteins is possible by addition of the tailpiece segment of IgM or IgA to the C-terminus of the Fc domain of IgGs, as exemplified for the IgM tailpiece segment in R. I. F. Smith and S. L. Morrison, Biotechnology 12: 683-688 (1994) and in R. I. F. Smith, et al., J. Immunol. 154: 2226-2236 (1995). These proteins are produced in insect cells or in mammalian cells such as COS-7 or CHO, purified by standard methodology, and are useful as tool, therapeutic, and diagnostic agents. Thus, these proteins are used to:

a) Determine the cleavage site of the N-terminal leader by amino acid sequence analysis of this processed recombinant protein.

b) Prepare polyclonal and monoclonal antibodies for:

1) Detection of PIGR-1 protein expression in different tissues and cell types.

2) Functional studies of PIGR-1 protein, such as induction of cell differentiation and proliferation, cytokine production, and cell death assays.

c) Test for agonist/antagonist activity when added to cultured cells and in animal models of immune disease.

d) Search for its ligand(s).

e) Establish screen assays for small molecule agonists or antagonists of PIGR-1 protein, which may be potential therapeutic and/or diagnostic agents.

All publications, including but not limited to patents and patent applications, cited in this specification are herein incorporated by reference as if each individual publication were specifically and individually indicated to be incorporated by reference herein as though fully set forth.

SEQUENCE LISTING <160> NUMBER OF SEQ ID NOS: 14 <210> SEQ ID NO: 1 <211> LENGTH: 2345 <212> TYPE: DNA <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 1 ccgggtcgac ccacgcgtcc gtgtgcagaa ggtgcaagcc agagctcagg ca gaacttcc 60 agagtgcatc tgggatctgc atttgccact ggttgcagat caggcggacg ag gagccggg 120 aaggcagagc catgtggctg ccccctgctc tgctccttct cagcctctca gg ctgtttct 180 ccatccaagg cccagagtct gtgagagccc cagagcaggg gtccctgacg gt tcaatgcc 240 actataagca aggatgggag acctacatta agtggtggtg ccgaggggtg cg ctgggata 300 catgcaagat cctcattgaa accagagggt cggagcaagg agagaagagt ga ccgtgtgt 360 ccatcaagga caatcagaaa gaccgcacgt tcactgtgac catggagggg ct caggcgag 420 atgacgcaga tgtttactgg tgtgggattg aaagaagagg acctgacctt gg gactcaag 480 tgaaagtgat tgttgaccca gagggagcgg cttccacaac agcaagctca cc taccaaca 540 gcaatatggc agtgttcatc ggctcccaca agaggaacca ctacatgctc ct ggtatttg 600 tgaaggtgcc catcttgctc atcttggtca ctgccatcct ctggttgaag gg gtctcaga 660 gggtccctga ggagccaggg gaacagccta tctacatgaa cttctccgaa cc tctgacta 720 aagacatggc cacttagaga gatggatctg cagagccttc ctgccctggc ca cgtttcca 780 gaagagactc gggctgtgga aggaacatct acgagtcctc gggatgcagt ga ctgagata 840 ggggccctgg gcctccgccc tggccttgga gctggtgggc acctccctgt tc tgcacagc 900 tcagggactt agccaggtcc tctcctgagc caccatcacc tcctggggtg cc agcacctg 960 ttctcttggt caggagctgt agagatggag ctcaagcact ggacgactct gt ccccactg 1020 ctggaataac tcgggcacag agcatgggac caaagtacag aaagaggttg gg ggagaccc 1080 ccccagccct agacttccat cattccggag accaactcaa caccgtcttt gc ctgagaac 1140 ctgatatatc cgtgttttta aatttttttt tttctagcaa agttgggttt ta atgactta 1200 tgttcatagg aaacctctct gatcccacac acaaggaggg tgattctggg at gagttcct 1260 ggttctaggg catgaggggc tggatggacc ctgtccccag ggaggacatg gc tctgagtc 1320 cacagggctg aggaggcaat gggaacctcc ctggcccggc ccggtggttg gc ctccccct 1380 cccacctctt cctcctccta gctccccaag ctccctgcct attcccccac ct ccgagggg 1440 ctgcagcttg ggagcctcct cagcatgaca gcttgggtct cctccccaaa ag agcctgtc 1500 aggcctcaag aaccacctcc aggtggggag ggcagtaacg aaaaccatcg ca ggaaatgg 1560 caccctccct tttcggtgat gttgaaatca tgttactaat gaaaactgtc ct agggaagt 1620 ggttctgtct cctcacaggc ttcacccacg gcgatgaggc ccttgaatgt gg tcactttg 1680 tgctgtatgg ttgagggacc ctcacaccaa agggaccttc ccatgtgaga tg tgctcccg 1740 cccccacctg cccacaagca aacacaccac acatgttcgg catgttgccg tt tgaacacc 1800 catgaggacg cctccaacct gctcttggtt ctaataggga gtactgactg tc agcagtgg 1860 ataaaggaga ggggaccctc tggtccctag catggcaccc agagcctccc ct cttcttgt 1920 ccttcagcca aagagaaact ttctctgact ttgaactgaa tttaggtctc tg gccaatga 1980 tgggcctgaa aattccataa tggccagaga ggagagttcg agcccggcta ag atcccctg 2040 agtcattctg tgagggacca agacccacag tccaccagcc ccagggccct ac ctcctgga 2100 atgctttcct ggatccagct tcccgaagat ccgaccagac ccagggagga cg gcaccgct 2160 ccgcgggagg gaaagccaaa gcatggtgct tcaccagctg gactcagggg cg aggggaca 2220 tgggcgcttg tcaacgtgat gtcattcttt tcccaccgtt tcttcctgtt ga tattcaat 2280 gaatccgtca atctctctgg aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aa aaaaaaaa 2340 aaaaa 2345 <210> SEQ ID NO: 2 <211> LENGTH: 201 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 2 Met Trp Leu Pro Pro Ala Leu Leu Leu Leu Se r Leu Ser Gly Cys Phe 1 5 10 15 Ser Ile Gln Gly Pro Glu Ser Val Arg Ala Pr o Glu Gln Gly Ser Leu 20 25 30 Thr Val Gln Cys His Tyr Lys Gln Gly Trp Gl u Thr Tyr Ile Lys Trp 35 40 45 Trp Cys Arg Gly Val Arg Trp Asp Thr Cys Ly s Ile Leu Ile Glu Thr 50 55 60 Arg Gly Ser Glu Gln Gly Glu Lys Ser Asp Ar g Val Ser Ile Lys Asp 65 70 75 80 Asn Gln Lys Asp Arg Thr Phe Thr Val Thr Me t Glu Gly Leu Arg Arg 85 90 95 Asp Asp Ala Asp Val Tyr Trp Cys Gly Ile Gl u Arg Arg Gly Pro Asp 100 105 110 Leu Gly Thr Gln Val Lys Val Ile Val Asp Pr o Glu Gly Ala Ala Ser 115 120 125 Thr Thr Ala Ser Ser Pro Thr Asn Ser Asn Me t Ala Val Phe Ile Gly 130 135 140 Ser His Lys Arg Asn His Tyr Met Leu Leu Va l Phe Val Lys Val Pro 145 1 50 1 55 1 60 Ile Leu Leu Ile Leu Val Thr Ala Ile Leu Tr p Leu Lys Gly Ser Gln 165 170 175 Arg Val Pro Glu Glu Pro Gly Glu Gln Pro Il e Tyr Met Asn Phe Ser 180 185 190 Glu Pro Leu Thr Lys Asp Met Ala Thr 195 200 <210> SEQ ID NO: 3 <211> LENGTH: 708 <212> TYPE: DNA <213> ORGANISM: HOMO SAPIENS <220> FEATURE: <221> NAME/KEY: UNSURE <222> LOCATION: (475)(620)(660) <400> SEQUENCE: 3 tgtgcagaag gtgcaagcca gagctcaggc agaacttcca gagtgcatct gg gatctgca 60 tttgccactg gttgcagatc aggcggacga ggagccggga aggcagagcc at gtggctgc 120 cccctgctct gctccttctc agcctctcag gctgtttctc catccaaggc cc agagtctg 180 tgagagcccc agagcagggg tccctgacgg ttcaatgcca ctataagcaa gg atgggaga 240 cctacattaa gtggtggtgc cgaggggtgc gctgggatac atgcaagatc ct cattgaaa 300 ccagagggtc ggagcaagga gagaagagtg accgtgtgtc catcaaggac aa tcagaaag 360 accgcacgtt cactgtgacc atggaggggc tcaggcgaga tgacgcagat gt ttactggt 420 gtgggattga aagaagagga cctgaccttg ggactcaagt gaaaattgat tg ttnaccca 480 gagggagcgg ctttccacaa cagcaaagct cacctaccaa cagcaatatg gc agtgttca 540 tcggctccca caagaggaac cactacatgc tcctggtatt tgtgaaggtg cc catcttgc 600 tcatcttggt caatgccatn ctctggttga aagggtctca gagggtccct ga ggagccan 660 gggaacagcc tatctacatg gacttctccg gactctgact aaagacat 708 <210> SEQ ID NO: 4 <211> LENGTH: 195 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <220> FEATURE: <221> NAME/KEY: UNSURE <222> LOCATION: (122)(170)(184) <400> SEQUENCE: 4 Met Trp Leu Pro Pro Ala Leu Leu Leu Leu Se r Leu Ser Gly Cys Phe 1 5 10 15 Ser Ile Gln Gly Pro Glu Ser Val Arg Ala Pr o Glu Gln Gly Ser Leu 20 25 30 Thr Val Gln Cys His Tyr Lys Gln Gly Trp Gl u Thr Tyr Ile Lys Trp 35 40 45 Trp Cys Arg Gly Val Arg Trp Asp Thr Cys Ly s Ile Leu Ile Glu Thr 50 55 60 Arg Gly Ser Glu Gln Gly Glu Lys Ser Asp Ar g Val Ser Ile Lys Asp 65 70 75 80 Asn Gln Lys Asp Arg Thr Phe Thr Val Thr Me t Glu Gly Leu Arg Arg 85 90 95 Asp Asp Ala Asp Val Tyr Trp Cys Gly Ile Gl u Arg Arg Gly Pro Asp 100 105 110 Leu Gly Thr Gln Val Lys Ile Asp Cys Xaa Pr o Arg Gly Ser Gly Phe 115 120 125 Pro Gln Gln Gln Ser Ser Pro Thr Asn Ser As n Met Ala Val Phe Ile 130 135 140 Gly Ser His Lys Arg Asn His Tyr Met Leu Le u Val Phe Val Lys Val 145 1 50 1 55 1 60 Pro Ile Leu Leu Ile Leu Val Asn Ala Xaa Le u Trp Leu Lys Gly Ser 165 170 175 Gln Arg Val Pro Glu Glu Pro Xaa Glu Gln Pr o Ile Tyr Met Asp Phe 180 185 190 Ser Gly Leu 195 <210> SEQ ID NO: 5 <211> LENGTH: 57 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 5 Ile Phe Gly Pro Glu Glu Val Asn Ser Val Gl u Gly Asn Ser Val Ser 1 5 10 15 Ile Thr Cys Tyr Tyr Pro Pro Thr Ser Val As n Thr Arg Lys Tyr Trp 20 25 30 Cys Arg Gln Gly Ala Arg Gly Cys Ile Thr Le u Ile Ser Ser Glu Gly 35 40 45 Tyr Val Ser Ser Lys Tyr Ala Gly Arg 50 55 <210> SEQ ID NO: 6 <211> LENGTH: 60 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 6 Pro Arg Ser Pro Thr Val Val Lys Gly Val Al a Gly Ser Ser Val Ala 1 5 10 15 Val Leu Cys Pro Tyr Asn Arg Lys Glu Ser Ly s Ser Ile Lys Tyr Trp 20 25 30 Cys Leu Trp Glu Gly Ala Gln Asn Gly Arg Cy s Pro Leu Leu Val Asp 35 40 45 Ser Glu Gly Trp Val Lys Ala Gln Tyr Glu Gl y Arg 50 55 60 <210> SEQ ID NO: 7 <211> LENGTH: 57 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 7 Leu Ser His Pro Met Thr Val Ala Gly Pro Va l Gly Gly Ser Leu Ser 1 5 10 15 Val Gln Cys Arg Tyr Glu Lys Glu His Arg Th r Leu Asn Lys Phe Trp 20 25 30 Cys Arg Pro Pro Gln Ile Leu Arg Cys Asp Ly s Ile Val Glu Thr Lys 35 40 45 Gly Ser Ala Gly Lys Arg Asn Gly Arg 50 55 <210> SEQ ID NO: 8 <211> LENGTH: 59 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 8 Ser Gln Lys Pro Ser Arg Asp Ile Cys Gln Ar g Gly Thr Ser Leu Thr 1 5 10 15 Ile Gln Cys Gln Val Asp Ser Gln Val Thr Me t Met Phe Trp Tyr Arg 20 25 30 Gln Gln Pro Gly Gln Ser Leu Thr Leu Ile Al a Thr Ala Asn Gln Gly 35 40 45 Ser Glu Ala Thr Tyr Glu Ser Gly Phe Val Il e 50 55 <210> SEQ ID NO: 9 <211> LENGTH: 55 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 9 Thr Gln Thr Pro Ala Ser Val Glu Val Ala Va l Gly Gly Thr Val Thr 1 5 10 15 Ile Lys Cys Gln Ala Ser Gln Ser Ile Ser Th r Tyr Leu Ser Trp Tyr 20 25 30 Gln Gln Lys Pro Gly Gln Arg Pro Lys Leu Le u Ile Tyr Arg Ala Ser 35 40 45 Thr Leu Ala Ser Gly Val Ser 50 55 <210> SEQ ID NO: 10 <211> LENGTH: 46 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 10 Ala Asn Leu Thr Asn Phe Pro Glu Asn Gly Th r Phe Thr Val Ile Leu 1 5 10 15 Asn Gln Leu Ser Gln Asp Asp Ser Gly Arg Ty r Lys Cys Gly Leu Gly 20 25 30 Ile Asn Ser Arg Gly Leu Ser Phe Asp Val Se r Leu Glu Val 35 40 45 <210> SEQ ID NO: 11 <211> LENGTH: 43 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 11 Leu Ser Leu Leu Glu Glu Pro Gly Asn Gly Th r Phe Thr Val Ile Leu 1 5 10 15 Asn Gln Leu Thr Ser Arg Asp Ala Gly Phe Ty r Trp Cys Leu Thr Asn 20 25 30 Gly Asp Thr Leu Trp Arg Thr Thr Val Glu Il e 35 40 <210> SEQ ID NO: 12 <211> LENGTH: 46 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 12 Val Ser Ile Arg Asp Ser Pro Ala Asn Leu Se r Phe Thr Val Thr Leu 1 5 10 15 Glu Asn Leu Thr Glu Glu Asp Ala Gly Thr Ty r Trp Cys Gly Val Asp 20 25 30 Thr Pro Trp Leu Arg Asp Phe His Asp Pro Il e Val Glu Val 35 40 45 <210> SEQ ID NO: 13 <211> LENGTH: 44 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 13 Asp Lys Phe Pro Ile Ser Arg Pro Asn Leu Th r Phe Ser Thr Leu Thr 1 5 10 15 Val Ser Asn Met Ser Pro Glu Asp Ser Ser Il e Tyr Leu Cys Ser Val 20 25 30 Glu Gly Glu Ala Gly Asp Thr Gln Tyr Phe Gl y Pro 35 40 <210> SEQ ID NO: 14 <211> LENGTH: 43 <212> TYPE: PRT <213> ORGANISM: HOMO SAPIENS <400> SEQUENCE: 14 Ser Arg Phe Lys Gly Ser Gly Ser Gly Thr Gl u Phe Thr Leu Thr Ile 1 5 10 15 Ser Gly Val Glu Cys Ala Asp Ala Ala Thr Ty r Tyr Cys Gln Gln Gly 20 25 30 Trp Ser Ser Ser Asn Val Glu Asn Val Phe Gl y 35 40 

What is claimed is:
 1. An isolated PIGR-1 polypeptide comprising the amino acid sequence of SEQ ID NO:2.
 2. The isolated polypeptide of claim 1 consisting of the amino acid sequence of SEQ ID NO:2. 